nohuman
Tags: human contamination decontamination scrubbing reads nohuman kraken2 sample-scope
Remove human reads from sequencing data using nohuman.
This subworkflow uses nohuman to identify and remove human reads from FASTQ files using a Kraken2 database built from Human Pangenome Reference Consortium (HPRC) genomes. It optionally downloads the database if not already available.
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end forward) |
r2 | Illumina R2 reads (paired-end reverse) |
se | Single-end Illumina reads |
lr | Long reads (ONT/PacBio) |
database: Path?
download_nohuman: Boolean
save_as_tarball: Boolean
| Name | Type | Description |
|---|---|---|
database | Path? | Path to nohuman database directory or tarball (ignored if download_nohuman is true) |
download_nohuman | Boolean | Boolean flag to download the database instead of using the provided path |
save_as_tarball | Boolean | Boolean flag to save downloaded database as tarball |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
scrubbed | FASTQ files with human reads removed |
scrub_report | Kraken2 classification report (optional) |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- nohuman_download - Download the nohuman database for human read removal.
- nohuman_run - Remove human reads from sequencing data.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
Kraken2
Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)